Proteins on microbial identification: past achievements, present state-of-the-art, and future challenges

The use of chemical analysis of microbial components, including proteins, became an important achievement in the 80’s of the last century to the microbial identification. This led a more objective microbial identification scheme, called chemotaxonomy, and the analytical tools used in the field are mainly 1D/2D gel electrophoresis, spectrophotometry, high-performance liquid chromatography, gas chromatography, and combined gas chromatography-mass spectrometry. The Edman degradation reaction was also applied to peptides sequence giving important insights to the microbial identification. The rapid development of these techniques, in association with knowledge generated by DNA sequencing and phylogeny based on rRNA gene and housekeeping genes sequences, boosted the microbial identification to an unparalleled scale. The recent results of mass spectrometry (MS), like Matrix-Assisted Laser Desorption/Ionisation Time-of-Flight (MALDI-TOF), for rapid and reliable microbial identification showed considerable promise. In addition, the technique is rapid, reliable and inexpensive in terms of labour and consumables when compared with other biological techniques. At present, MALDI-TOF MS adds an additional step for polyphasic identification which is essential when there is a paucity of characters or high DNA homologies for delimiting very close related species. The full impact of this approach is now being appreciated when more diverse species are studied in detail and successfully identified. However, even with the best polyphasic system, identification of some taxa remains time-consuming and determining what represents a species remains subjective. The possibilities opened with new and even more robust mass spectrometers combined with sound and reliable databases allow not only the microbial identification based on the proteome fingerprinting but also include de novo specific proteins sequencing as additional step. These approaches are pushing the boundaries in the microbial identification field.

Search for new phenomena in the dijet mass distribution using pp collision data at s√=8 TeV with the ATLAS detector

Dijet events produced in LHC proton--proton collisions at a center-of-mass energy s√=8 TeV are studied with the ATLAS detector using the full 2012 data set, with an integrated luminosity of 20.3 fb−1. Dijet masses up to about 4.5 TeV are probed. No resonance-like features are observed in the dijet mass spectrum. Limits on the cross section times acceptance are set at the 95% credibility level for various hypotheses of new phenomena in terms of mass or energy scale, as appropriate. This analysis excludes excited quarks with a mass below 4.09 TeV, color-octet scalars with a mass below 2.72 TeV, heavy W′ bosons with a mass below 2.45 TeV, chiral W∗ bosons with a mass below 1.75 TeV, and quantum black holes with six extra space-time dimensions with threshold mass below 5.82 TeV.

Measurement of exclusive γγ→ℓ+ℓ− production in proton--proton collisions at s√=7 TeV with the ATLAS detector

This Letter reports a measurement of the exclusive γγ→ℓ+ℓ−(ℓ=e,μ) cross-section in proton--proton collisions at a centre-of-mass energy of 7 TeV by the ATLAS experiment at the LHC, based on an integrated luminosity of 4.6 fb−1. For the electron or muon pairs satisfying exclusive selection criteria, a fit to the dilepton acoplanarity distribution is used to extract the fiducial cross-sections. The cross-section in the electron channel is determined to be σexcl.γγ→e+e−=0.428±0.035(stat.)±0.018(syst.) pb for a phase-space region with invariant mass of the electron pairs greater than 24 GeV, in which both electrons have transverse momentum pT>12 GeV and pseudorapidity |η|<2.4. For muon pairs with invariant mass greater than 20 GeV, muon transverse momentum pT>10 GeV and pseudorapidity |η|<2.4, the cross-section is determined to be σexcl.γγ→μ+μ−=0.628±0.032(stat.)±0.021(syst.) pb. When proton absorptive effects due to the finite size of the proton are taken into account in the theory calculation, the measured cross-sections are found to be consistent with the theory prediction.

Measurements of the Total and Differential Higgs Boson Production Cross Sections Combining the H→γγ and H→ZZ∗→4ℓ Decay Channels at s√=8 TeV with the ATLAS Detector

Measurements of the total and differential cross sections of Higgs boson production are performed using 20.3 fb−1 of pp collisions produced by the Large Hadron Collider at a center-of-mass energy of s√=8 TeV and recorded by the ATLAS detector. Cross sections are obtained from measured H→γγ and H→ZZ∗→4ℓ event yields, which are combined accounting for detector efficiencies, fiducial acceptances and branching fractions. Differential cross sections are reported as a function of Higgs boson transverse momentum, Higgs boson rapidity, number of jets in the event, and transverse momentum of the leading jet. The total production cross section is determined to be σpp→H=33.0±5.3(stat)±1.6(sys)pb. The measurements are compared to state-of-the-art predictions.

Measurement of the charge asymmetry in dileptonic decays of top quark pairs in pp collisions at s√=7 TeV using the ATLAS detector

A measurement of the top--antitop (tt¯) charge asymmetry is presented using data corresponding to an integrated luminosity of 4.6 fb−1 of LHC pp collisions at a centre-of-mass energy of 7 TeV collected by the ATLAS detector. Events with two charged leptons, at least two jets and large missing transverse momentum are selected. Two observables are studied: AℓℓC based on the identified charged leptons, and Att¯C, based on the reconstructed tt¯ final state. The asymmetries are measured to be AℓℓC=0.024±0.015 (stat.)±0.009 (syst.), Att¯C=0.021±0.025 (stat.)±0.017 (syst.). The measured values are in agreement with the Standard Model predictions.

Measurement of the inclusive jet cross-section in proton--proton collisions at s√=7 TeV using 4.5 fb−1 of data with the ATLAS detector

The inclusive jet cross-section is measured in proton--proton collisions at a centre-of-mass energy of 7 TeV using a data set corresponding to an integrated luminosity of 4.5 fb−1 collected with the ATLAS detector at the Large Hadron Collider in 2011. Jets are identified using the anti-kt algorithm with radius parameter values of 0.4 and 0.6. The double-differential cross-sections are presented as a function of the jet transverse momentum and the jet rapidity, covering jet transverse momenta from 100 GeV to 2 TeV. Next-to-leading-order QCD calculations corrected for non-perturbative effects and electroweak effects, as well as Monte Carlo simulations with next-to-leading-order matrix elements interfaced to parton showering, are compared to the measured cross-sections. A quantitative comparison of the measured cross-sections to the QCD calculations using several sets of parton distribution functions is performed.

Measurement of the tt¯ production cross-section as a function of jet multiplicity and jet transverse momentum in 7 TeV proton--proton collisions with the ATLAS detector

The tt¯ production cross-section dependence on jet multiplicity and jet transverse momentum is reported for proton--proton collisions at a centre-of-mass energy of 7 TeV in the single-lepton channel. The data were collected with the ATLAS detector at the CERN Large Hadron Collider and comprise the full 2011 data sample corresponding to an integrated luminosity of 4.6 fb−1. Differential cross-sections are presented as a function of the jet multiplicity for up to eight jets using jet transverse momentum thresholds of 25, 40, 60, and 80 GeV, and as a function of jet transverse momentum up to the fifth jet. The results are shown after background subtraction and corrections for all detector effects, within a kinematic range closely matched to the experimental acceptance. Several QCD-based Monte Carlo models are compared with the results. Sensitivity to the parton shower modelling is found at the higher jet multiplicities, at high transverse momentum of the leading jet and in the transverse momentum spectrum of the fifth leading jet. The MC@NLO+HERWIG MC is found to predict too few events at higher jet multiplicities.

Performance of the ATLAS muon trigger in pp collisions at s√=8 TeV

The performance of the ATLAS muon trigger system has been evaluated with proton--proton collision data collected in 2012 at the Large Hadron Collider at a centre-of-mass energy of 8 TeV. The performance was primarily evaluated using events containing a pair of muons from the decay of Z bosons. The efficiency is measured for the single-muon trigger for a kinematic region of the transverse momentum pT between 25 and 100 GeV, with a statistical uncertainty of less than 0.01% and a systematic uncertainty of 0.6%. The performance is also compared in detail to the predictions from simulation. The efficiency was measured over a wide pT range (a few GeV to several hundred GeV) by using muons from J/ψ mesons,W bosons, and top and antitop quarks. It showed highly uniform and stable performance.

Search for anomalous production of prompt same-sign lepton pairs and pair-produced doubly charged Higgs bosons with s√ = 8 TeV pp collisions using the ATLAS detector

A low-background inclusive search for new physics in events with same-sign dileptons is presented. The search uses proton--proton collisions corresponding to 20.3 fb−1 of integrated luminosity taken in 2012 at a centre-of-mass energy of 8 TeV with the ATLAS detector at the LHC. Pairs of isolated leptons with the same electric charge and large transverse momenta of the type e±e±,e±μ±, and μ±μ± are selected and their invariant mass distribution is examined. No excess of events above the expected level of Standard Model background is found. The results are used to set upper limits on the cross sections for processes beyond the Standard Model. Limits are placed as a function of the dilepton invariant mass within a fiducial region corresponding to the signal event selection criteria. Exclusion limits are also derived for a specific model of doubly charged Higgs boson production.

Identification and energy calibration of hadronically decaying tau leptons with the ATLAS experiment in pp collisions at s√=8 TeV

This paper describes the trigger and offline reconstruction, identification and energy calibration algorithms for hadronic decays of tau leptons employed for the data collected from pp collisions in 2012 with the ATLAS detector at the LHC center-of-mass energy s√ = 8 TeV. The performance of these algorithms is measured in most cases with Z decays to tau leptons using the full 2012 dataset, corresponding to an integrated luminosity of 20.3 fb−1. An uncertainty on the offline reconstructed tau energy scale of 2% to 4%, depending on transverse energy and pseudorapidity, is achieved using two independent methods. The offline tau identification efficiency is measured with a precision of 2.5% for hadronically decaying tau leptons with one associated track, and of 4% for the case of three associated tracks, inclusive in pseudorapidity and for a visible transverse energy greater than 20 GeV. For hadronic tau lepton decays selected by offline algorithms, the tau trigger identification efficiency is measured with a precision of 2% to 8%, depending on the transverse energy. The performance of the tau algorithms, both offline and at the trigger level, is found to be stable with respect to the number of concurrent proton--proton interactions and has supported a variety of physics results using hadronically decaying tau leptons at ATLAS.

Determination of spin and parity of the Higgs boson in the WW∗→eνμν decay channel with the ATLAS detector

Studies of the spin and parity quantum numbers of the Higgs boson in the WW∗→eνμν final state are presented, based on proton--proton collision data collected by the ATLAS detector at the Large Hadron Collider, corresponding to an integrated luminosity of 20.3 fb−1 at a centre-of-mass energy of s√=8 TeV. The Standard Model spin-parity JCP=0++ hypothesis is compared with alternative hypotheses for both spin and CP. The case where the observed resonance is a mixture of the Standard-Model-like Higgs boson and CP-even (JCP=0++) or CP-odd (JCP=0+−) Higgs boson in scenarios beyond the Standard Model is also studied. The data are found to be consistent with the Standard Model prediction and limits are placed on alternative spin and CP hypotheses, including CP mixing in different scenarios.

Search for high-mass diboson resonances with boson-tagged jets in proton-proton collisions at √s = 8TeV with the ATLAS detector

A search is performed for narrow resonances decaying into WW, WZ, or ZZ boson pairs using 20.3 fb−1 of proton--proton collision data at a centre-of-mass energy of s√ = 8 TeV recorded with the ATLAS detector at the Large Hadron Collider. Diboson resonances with masses in the range from 1.3 to 3.0 TeV are sought after using the invariant mass distribution of dijets where both jets are tagged as a boson jet, compatible with a highly boosted W or Z boson decaying to quarks, using jet mass and substructure properties. The largest deviation from a smoothly falling background in the observed dijet invariant mass distribution occurs around 2 TeV in the WZ channel, with a global significance of 2.5 standard deviations. Exclusion limits at the 95% confidence level are set on the production cross section times branching ratio for the WZ final state of a new heavy gauge boson, W′, and for the WW and ZZ final states of Kaluza--Klein excitations of the graviton in a bulk Randall--Sundrum model, as a function of the resonance mass. W′ bosons with couplings predicted by the extended gauge model in the mass range from 1.3 to 1.5 TeV are excluded at 95% confidence level.

Summary of the ATLAS experiment's sensitivity to supersymmetry after LHC Run 1-interpreted in the phenomenological MSSM

A summary of the constraints from the ATLAS experiment on R-parity-conserving supersymmetry is presented. Results from 22 separate ATLAS searches are considered, each based on analysis of up to 20.3 fb−1 of proton-proton collision data at centre-of-mass energies of s√=7 and 8 TeV at the Large Hadron Collider. The results are interpreted in the context of the 19-parameter phenomenological minimal supersymmetric standard model, in which the lightest supersymmetric particle is a neutralino, taking into account constraints from previous precision electroweak and flavour measurements as well as from dark matter related measurements. The results are presented in terms of constraints on supersymmetric particle masses and are compared to limits from simplified models. The impact of ATLAS searches on parameters such as the dark matter relic density, the couplings of the observed Higgs boson, and the degree of electroweak fine-tuning is also shown. Spectra for surviving supersymmetry model points with low fine-tunings are presented.

Study of (W/Z)H production and Higgs boson couplings using H -> WW* decays with the ATLAS detector

A search for Higgs boson production in association with a W or Z boson, in the H→ W W ∗ decay channel, is performed with a data sample collected with the ATLAS detector at the LHC in proton-proton collisions at centre-of-mass energies s√=7 TeV and 8 TeV, corresponding to integrated luminosities of 4.5 fb−1 and 20.3 fb−1, respectively. The WH production mode is studied in two-lepton and three-lepton final states, while two- lepton and four-lepton final states are used to search for the ZH production mode. The observed significance, for the combined W H and ZH production, is 2.5 standard deviations while a significance of 0.9 standard deviations is expected in the Standard Model Higgs boson hypothesis. The ratio of the combined W H and ZH signal yield to the Standard Model expectation, μ V H , is found to be μ V H  = 3.0 − 1.1 + 1.3 (stat.) − 0.7 + 1.0 (sys.) for the Higgs boson mass of 125.36 GeV. The W H and ZH production modes are also combined with the gluon fusion and vector boson fusion production modes studied in the H → W W ∗ → ℓνℓν decay channel, resulting in an overall observed significance of 6.5 standard deviations and μ ggF + VBF + VH = 1. 16 − 0.15 + 0.16 (stat.) − 0.15 + 0.18 (sys.). The results are interpreted in terms of scaling factors of the Higgs boson couplings to vector bosons (κ V ) and fermions (κ F ); the combined results are: |κ V | = 1.06 − 0.10 + 0.10 , |κ F | = 0. 85 − 0.20 + 0.26 .

Measurement of differential J/psi production cross sections and forward-backward ratios in p plus Pb collisions with the ATLAS detector

Measurements of differential cross sections for J/ψ production in p+Pb collisions at sNN−−−−√=5.02 TeV at the CERN Large Hadron Collider with the ATLAS detector are presented. The data set used corresponds to an integrated luminosity of 28.1 nb−1. The J/ψ mesons are reconstructed in the dimuon decay channel over the transverse momentum range 8of-mass rapidity range −2.87of the distance between the J/ψ decay vertex and the event primary vertex. The differential cross section for production of nonprompt J/ψ is compared to a FONLL calculation that does not include nuclear effects. Forward-backward production ratios are presented and compared to theoretical predictions. These results complement previously published results by covering a region of higher transverse momentum and more central rapidity. They thus constrain the kinematic dependence of nuclear modifications of charmonium and b-quark production in p+Pb collisions.